Digital Commons Network^™

Sex-Biased Gene Flow Among Elk In The Greater Yellowstone Ecosystem, Brian K. Hand, Shanyuan Chen, Neil Anderson, Albano Beja-Pereira, Paul C. Cross, Michael Ebinger, Hank Edwards, Robert A. Garrott, Marty D. Kardos, Matt Kauffman, Erin L. Landguth, Arthur Middleton, Brandon Scurlock, P.J. White, Pete Zager, Michael K. Schwartz, Gordon Luikart

United States Geological Survey: Staff Publications

We quantified patterns of population genetic structure to help understand gene flow among elk populations across the Greater Yellowstone Ecosystem. We sequenced 596 base pairs of the mitochondrial control region of 380 elk from eight populations. Analysis revealed high mitochondrial DNA variation within populations, averaging 13.0 haplotypes with high mean gene diversity (0.85). The genetic differentiation among populations for mitochondrial DNA was relatively high (FST = 0.161; P = 0.001) compared to genetic differentiation for nuclear microsatellite data (FST = 0.002; P = 0.332), which suggested relatively low female gene flow among populations. The estimated ratio of male to female …

A Metapopulation Model For Sylvatic T. Cruzi Transmission With Vector Migration, Christopher Kribs, Britnee Crawford

Mathematics Faculty Publications - Archive

This study presents a metapopulation model for the sylvatic transmission of Trypanosoma cruzi, the etiological agent of Chagas' disease, across multiple geographical regions and multiple overlapping host-vector transmission cycles. Classical qualitative analysis of the model and several submodels focuses on the parasite's basic reproductive number, illustrating how vector migration across patches and multiple transmission routes to hosts (including vertical transmission) determine the infection's persistence in each cycle. Numerical results focus on trends in endemic [equilibrium] persistence levels as functions of vector migration rates, and highlight the significance of the different epidemiological characteristics of transmission in each of the three regions.

Oligomask: A Framework For Assessing And Removing The Effect Of Genetic Variants On Microarray Probes, Daniel Bottomly, Beth Wilmot, Shannon K. Mcweeney

The R Journal

As expression microarrays are typically designed relative to a reference genome, any individual genetic variant that overlaps a probe’s genomic position can possibly cause a reduction in hybridization due to the probe no longer being a perfect match to a given sample’s mRNA at that locus. If the samples or groups used in a microarray study differ in terms of genetic variants, the results of the microarray experiment can be negatively impacted. The oligoMask package is an R/SQLite framework which can utilize publicly available genetic variants and works in conjunction with the oligo package to read in the expression data …

Modeling The Transmission Dynamics Of Typhoid In Malaria Endemic Settings, Steady Mushayabasa, Claver P. Bhunu, Ngoni A. Mhlanga

Applications and Applied Mathematics: An International Journal (AAM)

Typhoid and malaria co-infection is a major public health problem in many developing countries. In this paper, a deterministic model for malaria and typhoid co-infection is proposed and analyzed. It has been established that the model exhibits a backward bifurcation phenomenon. Overall, the study reveals that a typhoid outbreak in malaria endemic settings may lead to higher cumulative cases of dually-infected individuals displaying clinical symptoms of both infections than singly-infected individuals displaying clinical symptoms of either malaria or typhoid.

Partially-Latent Class Models (Plcm) For Case-Control Studies Of Childhood Pneumonia Etiology, Zhenke Wu, Maria Deloria-Knoll, Laura L. Hammitt, Scott L. Zeger

Johns Hopkins University, Dept. of Biostatistics Working Papers

In population studies on the etiology of disease, one goal is the estimation of the fraction of cases attributable to each of several causes. For example, pneumonia is a clinical diagnosis of lung infection that may be caused by viral, bacterial, fungal, or other pathogens. The study of pneumonia etiology is challenging because directly sampling from the lung to identify the etiologic pathogen is not standard clinical practice in most settings. Instead, measurements from multiple peripheral specimens are made. This paper considers the problem of estimating the population etiology distribution and the individual etiology probabilities. We formulate the scientific …

California Drought: A Need For Agricultural Revolution In The Golden State, Benjamin Clinkinbeard

2014 Student Theses

California is in a drought State of Emergency, which is fueling negative social and economic consequences. After multiple years of below average rainfall, California has arrived at one of the most severe droughts in recorded history. Climate change is upon the Golden State, and the ugly consequences need to encourage citizens to spur green movements combating environmental destruction. The agriculture industry is in need of drastic change in order to secure a future that includes clean water, and fresh food for a growing population. Currently, the agricultural techniques practiced are far from sustainable. Adopting a new ideal on what it …

Growing Roots: Gardening As A Means To Mitigate Urban Poverty And Its Symptoms, Maeve Bassett

2014 Student Theses

Urban gardening has become a very popular trend in the last few years in both affluent neighborhoods as a form of relaxation and in impoverished areas as a form of hunger relief. In impoverished areas, urban gardens are usually exclusively advertised as a solution to limited food access; however, there is a naïve belief that these gardens are effective forms of mass food production. Presently, these gardens are not productive enough to globally effect food production and the environment. However, to the communities surrounding the gardens, the effects are immense. Urban gardens are cheap and effective solutions for many of …

The Dimerization Domain In Dape Enzymes Is Required For Catalysis, Boguslaw Nocek, Anna Starus, Magdalena Makowska-Grzyska, Blanca Gutierrez, Stephen Sanchez, Robert Jedrzejczak, Jamey C. Mack, Kenneth W. Olsen, Andzrej Joachimiak, Richard C. Holz

Chemistry Faculty Research and Publications

The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Therefore dap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) converts N-succinyl-L,L-diaminopimelic acid to L,Ldiaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role …

Reclaiming The Efficacy Of Β-Lactam–Β-Lactamase Inhibitor Combinations: Avibactam Restores The Susceptibility Of Cmy-2-Producing Escherichia Coli To Ceftazidime, Krisztina M. Papp-Wallace, Marisa L. Winkler, Julian A. Gatta, Magdalena A. Taracila, Sujatha Chilakala, Yan Xu, J. Kristie Johnson, Robert A. Bonomo

Chemistry Faculty Publications

CMY-2 is a plasmid-encoded Ambler class C cephalosporinase that is widely disseminated in Enterobacteriaceae and is responsible for expanded-spectrum cephalosporin resistance. As a result of resistance to both ceftazidime and β-lactamase inhibitors in strains carrying blaCMY, novel β-lactam–β-lactamase inhibitor combinations are sought to combat this significant threat to β-lactam therapy. Avibactam is a bridged diazabicyclo [3.2.1]octanone non-β-lactam β-lactamase inhibitor in clinical development that reversibly inactivates serine β-lactamases. To define the spectrum of activity of ceftazidime-avibactam, we tested the susceptibilities of Escherichia coli clinical isolates that carry blaCMY-2 or blaCMY-69 and investigated the inactivation kinetics of CMY-2. Our analysis showed that …

The Effects Of Anthropogenic Nitrogen On Public Health, Grace Fowler, John Sears

CLAS: Colby Liberal Arts Symposium

Human activities that add nitrogen to the environment are dramatically affecting the nitrogen cycle. Advancements in the production of reactive nitrogen in the 1950s rapidly increased the production of nitrogen fertilizers used in agricultural food production, a significant source of nitrogen in the cycle. Increased crop yields have been tied to the rapidly ascending human population and associated environmental impacts, and the alteration of the nitrogen cycle itself is associated with documented environmental detriment. A review of the history of ascending anthropogenic nitrogen production in agricultural and industrial processes also reveals its role in negatively altering greenhouse gas levels, spreading …

Cyanide Toxicokinetics: The Behavior Of Cyanide, Thiocyanate And 2-Amino-2-Thiazoline-4-Carboxylic Acid In Multiple Animal Models, Raj K. Bhandari, Robert P. Oda, Ilona Petrikovics, David E. Thompson, Matthew Brenner, Sari B. Mahon, Vikhyat S. Bebarta, Gary A. Rockwood, Brian A. Logue

Chemistry and Biochemistry Faculty Publications

Cyanide causes toxic effects by inhibiting cytochrome c oxidase, resulting in cellular hypoxia and cytotoxic anoxia, and can eventually lead to death. Cyanide exposure can be verified by direct analysis of cyanide concentrations or analyzing its metabolites, including thiocyanate (SCN⁻) and 2-amino-2-thiazoline-4-carboxylic acid (ATCA) in blood. To determine the behavior of these markers following cyanide exposure, a toxicokinetics study was performed in three animal models: (i) rats (250–300 g), (ii) rabbits (3.5–4.2 kg) and (iii) swine (47–54 kg). Cyanide reached a maximum in blood and declined rapidly in each animal model as it was absorbed, distributed, metabolized and …

Mapping Of Pathogenic Vibrio Spp. Densities In The Gulf Of Mexico And Their Relationship To Fecal Indicators Used In Oyster Harvest Regulation, Morgan Taylor

Honors Capstones

No abstract provided.

The Role Of Stress-Activated Protein Kinases In Parasites, Tamara Kreiss

Theses, Dissertations and Culminating Projects

Lymphatic filariasis and leishmaniasis are neglected tropical diseases that are caused by nematode and protozoal parasites. These diseases cause disfiguration, leaving their host socially marked, and in some cases cause more severe disease that can lead to death. These infections, which tend to persist for long periods of time, also lead to bacterial and fungal co-infections, which further exacerbate the disease. Currently there are insufficient treatment options. Current therapies are often too expensive, have toxicity associated with them and are subjected to growing resistance amongst parasite populations. In this thesis I investigated two potential drug targets. The first, is the …

Anthropogenic Disturbance Of The Herpetofauna In The Northeast Us : Wildlife Disease And Habitat Modification, Paola Dolcemascolo

Theses, Dissertations and Culminating Projects

Herpetofauna represent some of the most striking examples of the consequences of human impact on biotic communities. They experience the full range of anthropogenically-derived stressors: habitat loss, habitat modification and degradation, pollution, collection for food and the pet trade, nuisance killings, road mortality, and disease. In this study, I examined some of the main threats faced by herpetofauna of the Northeastern United States and their implications for management of reptile and amphibians in New Jersey. I first used molecular techniques to document and assess the prevalence of two amphibian diseases, chytridiomycosis (caused by the chytrid fungus, Batrachochytrium dendrobatidis) and Ranavirus, …

Adapting To A Changing Climate: Local Drivers For Policy Response, Andrew J. Bilich

Honors Scholar Theses

Responding to the present and looming effects of global climate change presents a challenging task for policymakers at all levels of governance. The outcomes of climate change do present serious adaptation problems for global policy makers, but the implications of climate change are more immediately experienced by local communities and policy makers. Historical policymaking models suggest that economic well-being is an influential driver in local policy adoption. This particular analysis explores the relationship between economic variables and the development of climate adaptation policies by Connecticut municipalities. To test the degree of interaction present, adaptation policy data in the form of …

Assessing The Impacts Of Unrestricted Pesticide Use In Small-Scale Agriculture On Water Quality And Associated Human Health And Ecological Implications In An Indigenous Village In Rural Panam[Aacute], Sarah Louise Watson

USF Tampa Graduate Theses and Dissertations

In 2014, the global pesticide industry's projected worth is $52 billion and by 2020, the developing world will make up one-third of the world's chemical production and consumption. Pesticides can have unintended negative consequences for human health and the environment, especially in the developing world where regulations are loose or nonexistent. One country with unrestricted use of pesticides is Panam[aacute], especially in Santa Rosa de Cucunatí. In this indigenous village, small-scale farmers and ranchers spray paraquat, glyphosate, picloram, and 2,4-D at higher elevations than the spring water source of a gravity-fed water system, the river, and the village. The objective …

The Dimerization Domain In Dape Enzymes Is Required For Catalysis, Boguslaw Nocek, Anna Starus, Magdalena Makowska-Grzyska, Blanca Gutierrez, Stephen Sanchez, Robert Jedrzejczak, Jamey C. Mack, Kenneth W. Olsen, Andrzej Joachimiak, Richard C. Holz

Chemistry: Faculty Publications and Other Works

The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Thereforedap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) convertsN-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role …

Modeling Dengue Transmission And Vaccination, Abhishek Pandey

All Dissertations

Dengue is one of the most rapidly spreading mosquito-borne viral diseases in the world and inflicts significant health, economic and social burdens on populations. In this dissertation, I studied different aspects of modeling of dengue and vector-borne diseases in general. Among various dengue models that have appeared in literature, some explicitly model the mosquito population, while others model them implicitly. In spite of extensive use of both modeling approaches, little guidance exists for which type of model should be preferred. I developed a Bayesian approach that uses a Markov chain Monte Carlo (MCMC) method to fit disease models to epidemiological …

Health Hazards In Rental Housing: An Overview Of Clark County, Nevada, Amanda Nicole Sokolowsky

UNLV Theses, Dissertations, Professional Papers, and Capstones

A wide range of health conditions are associated with housing conditions, including asthma, respiratory infections, injuries, mental health issues, and lead poisoning. People in modern societies spend more than 90% of their time indoors, the vast majority of which is spent at home. Therefore, any new information on housing related health hazards in a population provides an opportunity for a new prevention program. Reports have shown that rental properties have more health related hazards than owner occupied housing, and rental properties are frequently occupied by low-income and minority individuals. This descriptive study intended to provide an overview of housing related …

Assessing The Impact Of Misclassification When Comparing Prevalence Data: A Novel Sensitivity Analysis Approach, Ninet Sinaii, Sean D. Cleary, Pamela Stratton

Epidemiology Faculty Publications

Background: A simple sensitivity analysis technique was developed to assess the impact of misclassification and verify observed prevalence differences between distinct populations.

Methods: The prevalence of self-reported comorbid diseases in 4,331 women with surgically-diagnosed endometriosis was compared to published clinical and population-based prevalence estimates. Disease prevalence misclassification was assessed by assuming over-reporting in the study sample and under-reporting in the general (comparison) population. Over- and under-reporting by 10%, 25%, 50%, 75%, and 90% was used to create a 5×5 table for each disease. The new prevalences represented by each table cell were compared by p-values, prevalence odds ratios, and 95% …

Developing Transmissible Vaccines For Animal Infections: Intrinsically Safe Designs And A Staged Transparent Development Process Will Be Essential, Daniel G. Streiker, Megan E. Griffiths, Rustom Antia, Laura Bergner, Peter Bowman, Maria Vitoria Dos Santos De Moraes, Kevin Esvelt, Mike Famulare, Amy T. Gilbert, Biao He, Michael A. Jarvis, David A. Kennedy, Jennifer Kuzma, Carolyne Nasi,Iyu Wanyonyi, Christopher Remien, Tonie Rocke, Kyle Rosenke, Courtney Schreiner, Justin Sheen, David Simons, Ivet A. Yordanova, James J. Bull, Scott L. Nuismer

United States Department of Agriculture Wildlife Services: Staff Publications

Developing Transmissible Vaccines for Animal Infections: Intrinsically Safe Designs and a Staged Transparent Development Process Will Be Essential

Intrinsically safe, biologically compelling vaccine designs

Pahsed development must incorporate checkpoints and engagement

Staged development with established checkpoints

Wquitable partnerships with international governance

Toward deployment

Workshop organization

Seven proposed commitm ents for the responsible development of transmissible vaccines for infectious disease control in animals

Evolutionary outcomes of vaccine transmission depend on the viral vector and the genetic modifications introduced

Venue-Based Recruitment Of Women At Elevated Risk For Hiv: An Hiv Prevention Trials Network Study, Danielle F. Haley, Carol E. Golin, Wafaa M. El-Sadr, James P. Hughes, Jing Wang, Irene Kuo, +13 Additional Authors

Epidemiology Faculty Publications

Background: The challenge of identifying and recruiting U.S. women at elevated risk for HIV acquisition impedes prevention studies and services. HIV Prevention Trials Network (HPTN) 064 was a U.S. multisite, longitudinal cohort study designed to estimate HIV incidence among women living in communities with prevalent HIV and poverty. Venue-based sampling (VBS) methodologies and participant and venue characteristics are described.

Methods: Eligible women were recruited from 10 U.S. communities with prevalent HIV and poverty using VBS. Participant eligibility criteria included age 18–44 years, residing in a designated census tract/zip code, and self-report of at least one high-risk personal and/or male sexual …

Circulation, Vol. 19, No. 1, Center For Coastal Physical Oceanography, Old Dominion University, John M. Klinck, Eileen E. Hofmann

CCPO Circulation

Spring 2014 issue of Circulation, featuring the article "Theoretical Models of Marine Infectious Diseases and the Effects of Climate Variability" by John Klinck and Eileen Hofmann

2014 (Spring), University Of Dayton. Department Of Mathematics

Colloquia

Abstracts of the talks given at the 2014 Spring Colloquium.

Analyzing Cholera Dynamics In Homogeneous And Heterogeneous Environments, Drew Posny

Mathematics & Statistics Theses & Dissertations

Cholera continues to be a serious public health concern in developing countries and the global increase in the number of reported outbreaks suggests that activities to control the diseases and surveillance programs to identify or predict the occurrence of the next outbreaks are not adequate. Mathematical models play a critical role in predicting and understanding disease mechanisms, and have long provided basic insights in the possible ways to control infectious diseases. This dissertation is concerned with mathematical modeling and analysis of cholera dynamics. First, we study an autonomous model in a homogeneous environment with added controls that involves both direct …

Synthesis And Evaluation Of 3-Aryl-4(1h)-Quinolones As Orally Active Antimalarials: Overcoming Challenges In Solubility, Metabolism, And Bioavailability, Andrii Monastyrskyi

USF Tampa Graduate Theses and Dissertations

Infectious diseases are the second leading cause of deaths in the world with malaria being responsible for approximately the same amount of deaths as cancer in 2012. Despite the success in malaria prevention and control measures decreasing the disease mortality rate by 45% since 2000, the development of single-dose therapeutics with radical cure potential is required to completely eradicate this deadly disease. Targeting multiple stages of the malaria parasite is becoming a primary requirement for new candidates in antimalarial drug discovery and development. Recently, 4(1H)-pyridone, 4(1H)-quinolone, 1,2,3,4-tetrahydroacridone, and phenoxyethoxy-4(1H)-quinolone chemotypes have been shown to be antimalarials with blood stage activity, …

Lead (Pb) Contamination Of Water Drawn From Pitcher Pumps In Eastern Madagascar, David Bradlee Akers

USF Tampa Graduate Theses and Dissertations

Access to safe water supply--a major determinant of public health--is less than 50% in Madagascar, and access to piped, treated water remains out of reach financially for many in the urban and peri-urban areas where available. The Self-supply option of the Pitcher Pump has been meeting the need for household water in coastal areas of Madagascar since the early 1960s and has proven a sustainable option for many. These pumps make use of leaded components in the construction, however, which may pose a health risk for heavy metal intoxication and therefore cause the water to be unsafe for drinking and …

Fuzzy Logic Ideas Can Help In Explaining Kahneman And Tversky's Empirical Decision Weights, Joe Lorkowski, Vladik Kreinovich

Departmental Technical Reports (CS)

Analyzing how people actually make decisions, the Nobelist Daniel Kahneman and his co-author Amos Tversky found out that instead of maximizing the expected gain, people maximize a weighted gain, with weights determined by the corresponding probabilities. The corresponding empirical weights can be explained qualitatively, but quantitatively, these weights remains largely unexplained. In this paper, we show that with a surprisingly high accuracy, these weights can be explained by fuzzy logic ideas.

Benefits And Barriers To Hiv Testing In A Population Of Federal Detention Inmates, Nicole A. Knight

Loma Linda University Electronic Theses, Dissertations & Projects

Voluntary HIV testing in combination with early medical intervention has been shown to be effective in reducing the rate of new infections and improving the health and life expectancy of those living with HIV. There are however several high-risk populations in the US that remain largely unreached by HIV testing efforts, some of which could be reached while they spend time in prison or jail. Per current Bureau of Prisons (BOP) policy, HIV testing is routinely offered only to “high risk” pretrial and sentenced inmates. We conducted a cross-sectional study with 721 pretrial and sentenced inmates who entered a large …

Gene And Protein Sequence Optimization For High-Level Production Of Fully Active And Aglycosylated Lysostaphin In Pichia Pastoris, Hongliang Zhao, Kristina Blazanovic, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold

Dartmouth Scholarship

Lysostaphin represents a promising therapeutic agent for the treatment of staphylococcal infections, in particular those of methicillin-resistant Staphylococcus aureus (MRSA). However, conventional expression systems for the enzyme suffer from various limitations, and there remains a need for an efficient and cost-effective production process to facilitate clinical translation and the development of nonmedical applications. While Pichia pastoris is widely used for high-level production of recombinant proteins, there are two major barriers to the production of lysostaphin in this industrially relevant host: lack of expression from the wild-type lysostaphin gene and aberrant glycosylation of the wild-type protein sequence. The first barrier can …